JAL-845 applet colour by tree; translate as cDNA; pull up history list

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 3ccf88c..1ef1d07 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -13,7 +13,7 @@ import org.junit.Test;
 
 public class SequenceTest
 {
-  Sequence seq;
+  SequenceI seq;
 
   @Before
   public void setUp()
@@ -21,6 +21,21 @@ public class SequenceTest
     seq = new Sequence("FER1", "AKPNGVL");
   }
   @Test
+  public void testInsertGapsAndGapmaps()
+  {
+    SequenceI aseq = seq.deriveSequence();
+    aseq.insertCharAt(2, 3, '-');
+    aseq.insertCharAt(6, 3, '-');
+    assertEquals("Gap insertions not correct", "AK---P---NGVL",
+            aseq.getSequenceAsString());
+    List<int[]> gapInt = aseq.getInsertions();
+    assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]);
+    assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
+    assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
+    assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
+  }
+
+  @Test
   public void testGetAnnotation()
   {
     // initial state returns null not an empty array
@@ -95,7 +110,7 @@ public class SequenceTest
   @Test
   public void testAddAlignmentAnnotation()
   {
-    assertNull(seq.annotation);
+    assertNull(seq.getAnnotation());
     final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
             "b", 2d);
     assertNull(annotation.sequenceRef);
@@ -247,4 +262,52 @@ public class SequenceTest
     seq.createDatasetSequence();
     assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(seq.gapMap()));
   }
+
+  /**
+   * Test the method that gets sequence features, either from the sequence or
+   * its dataset.
+   */
+  @Test
+  public void testGetSequenceFeatures()
+  {
+    SequenceI seq = new Sequence("test", "GATCAT");
+    seq.createDatasetSequence();
+
+    assertNull(seq.getSequenceFeatures());
+
+    /*
+     * SequenceFeature on sequence
+     */
+    SequenceFeature sf = new SequenceFeature();
+    seq.addSequenceFeature(sf);
+    SequenceFeature[] sfs = seq.getSequenceFeatures();
+    assertEquals(1, sfs.length);
+    assertSame(sf, sfs[0]);
+
+    /*
+     * SequenceFeature on sequence and dataset sequence; returns that on
+     * sequence
+     */
+    SequenceFeature sf2 = new SequenceFeature();
+    seq.getDatasetSequence().addSequenceFeature(sf2);
+    sfs = seq.getSequenceFeatures();
+    assertEquals(1, sfs.length);
+    assertSame(sf, sfs[0]);
+
+    /*
+     * SequenceFeature on dataset sequence only
+     */
+    seq.setSequenceFeatures(null);
+    sfs = seq.getSequenceFeatures();
+    assertEquals(1, sfs.length);
+    assertSame(sf2, sfs[0]);
+
+    /*
+     * Corrupt case - no SequenceFeature, dataset's dataset is the original
+     * sequence. Test shows no infinite loop results.
+     */
+    seq.getDatasetSequence().setSequenceFeatures(null);
+    seq.getDatasetSequence().setDatasetSequence(seq); // loop!
+    assertNull(seq.getSequenceFeatures());
+  }
 }